8BD3
Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, FA (1, 7) | Chlorophyll a-b binding protein, chloroplastic | polymer | 214 | 23060.1 | 2 | UniProt (A0A2P6TPU9) Pfam (PF00504) | Chlorella ohadii | |
| 2 | B, D, HA, JA, M... (2, 4, G, 9, q...) | Chlorophyll a-b binding protein, chloroplastic | polymer | 222 | 23850.7 | 6 | UniProt (A0A2P6TDA6) Pfam (PF00504) | Chlorella ohadii | |
| 3 | C, E, GA, IA, T... (3, 5, N, 8, p...) | Chlorophyll a-b binding of LHCII | polymer | 221 | 23847.9 | 6 | Chlorella ohadii | ||
| 4 | EA, F (6, 0) | Chlorophyll a-b binding of LHCII | polymer | 217 | 23455.5 | 2 | Chlorella ohadii | ||
| 5 | G, KA (A, a) | Photosystem II protein D1 | polymer | 336 | 37230.3 | 2 | UniProt (W8SIR2) | Chlorella ohadii | |
| 6 | H, LA (B, b) | Photosystem II CP47 reaction center protein | polymer | 504 | 55754.3 | 2 | UniProt (W8TIK4) | Chlorella ohadii | |
| 7 | I, MA (C, c) | Photosystem II CP43 reaction center protein | polymer | 448 | 49161.1 | 2 | UniProt (A0A076EAP1) | Chlorella ohadii | PSII 43 kDa protein,Protein CP-43 |
| 8 | J, NA (D, d) | Photosystem II D2 protein | polymer | 342 | 38459.9 | 2 | UniProt (W8SYD4) | Chlorella ohadii | |
| 9 | K, OA (E, e) | Cytochrome b559 subunit alpha | polymer | 81 | 9204.3 | 2 | UniProt (W8SU91) | Chlorella ohadii | PSII reaction center subunit V |
| 10 | L, PA (F, f) | Cytochrome b559 subunit beta | polymer | 37 | 4262.1 | 2 | UniProt (P56310) | Chlorella ohadii | PSII reaction center subunit VI |
| 11 | N, RA (H, h) | Photosystem II reaction center protein H | polymer | 67 | 7223.4 | 2 | UniProt (W8SIT0) | Chlorella ohadii | |
| 12 | O, SA (I, i) | Photosystem II reaction center protein I | polymer | 34 | 3871.5 | 2 | UniProt (A0A5P4ND48) | Chlorella ohadii | PSII-I,PSII 4.8 kDa protein |
| 13 | P, TA (J, j) | Photosystem II reaction center protein J | polymer | 38 | 3813.5 | 2 | UniProt (W8TIH6) | Chlorella ohadii | |
| 14 | Q, UA (K, k) | Photosystem II reaction center protein K | polymer | 37 | 4140.0 | 2 | UniProt (P56348) | Chlorella ohadii | PSII-K |
| 15 | R, VA (L, l) | Photosystem II reaction center protein L | polymer | 37 | 4260.0 | 2 | UniProt (P56339) | Chlorella ohadii | PSII-L |
| 16 | S, WA (M, m) | Photosystem II reaction center protein M | polymer | 57 | 5621.9 | 2 | UniProt (A0A5P4NAV9) | Chlorella ohadii | |
| 17 | U, YA (O, o) | Chloroplast oxygen-evolving enhancer protein 1 | polymer | 240 | 25449.5 | 2 | UniProt (A0A5P4NF37) | Chlorella ohadii | |
| 18 | V, ZA (R, r) | Chlorophyll a b binding CP29 | polymer | 236 | 25803.7 | 2 | Chlorella ohadii | ||
| 19 | AB, W (S, s) | Chlorophyll a b-binding CP26 | polymer | 257 | 27369.8 | 2 | Chlorella ohadii | ||
| 20 | BB, X (T, t) | Photosystem II reaction center protein T | polymer | 30 | 3476.2 | 2 | UniProt (P56327) | Chlorella ohadii | PSII-T |
| 21 | CB, Y (V, v) | Photosystem II reaction center protein Ycf12 | polymer | 32 | 3319.0 | 2 | UniProt (A0A076EAR3) | Chlorella ohadii | |
| 22 | DB, Z (W, w) | Photosystem II reaction center W protein | polymer | 60 | 6623.4 | 2 | Chlorella ohadii | ||
| 23 | AA, EB (X, x) | Photosystem II reaction center protein X | polymer | 37 | 3526.0 | 2 | Chlorella ohadii | ||
| 24 | BA, FB (Y, y) | Multifunctional fusion protein | polymer | 221 | 23864.0 | 2 | UniProt (A0A2P6U5M3) Pfam (PF00504) | Chlorella ohadii | |
| 25 | CA, GB (Z, z) | Photosystem II reaction center protein Z | polymer | 62 | 6727.1 | 2 | UniProt (W8SKL0) | Chlorella ohadii | |
| 26 | DA, HB (U, u) | Chloroplast oxygen-evolving enhancer protein 3 | polymer | 144 | 15948.1 | 2 | UniProt (A0A5P4NB29) | Chlorella ohadii | |
| 27 | IB, KB (Q1, q1) | Chloroplast PsbY | polymer | 34 | 3697.3 | 2 | UniProt (A0A5P4NEE0) | Chlorella ohadii | |
| 28 | JB, LB (P1, p1) | Chloroplast photosystem II 10 kDa protein | polymer | 108 | 11657.3 | 2 | UniProt (A0A5P4NAS4) | Chlorella ohadii | |
| 29 | MB, NB (F1, f1) | Photosystem II oxygen evolving enhancer 2 | polymer | 188 | 20416.8 | 2 | Chlorella ohadii | ||
| 30 | AF, AL, AQ, AR, BE... (5, N, 8, 9, 4...) | CHLOROPHYLL B | non-polymer | 907.5 | 122 | Chemie (CHL) | |||
| 31 | AC, AE, AG, AI, AJ... (1, 4, 6, C, D...) | CHLOROPHYLL A | non-polymer | 893.5 | 270 | Chemie (CLA) | |||
| 32 | ABA, AN, BO, CC, CG... (y, S, Y, 1, 6...) | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL | non-polymer | 568.9 | 36 | Chemie (LUT) PubChem (177565809) PubChem (181579) PubChem (177696530) PubChem (24728610) PubChem (25202165) PubChem (441664) PubChem (44481270) PubChem (25245095) PubChem (46835684) PubChem (53477744) PubChem (53477774) PubChem (53477760) PubChem (57922343) PubChem (6325550) PubChem (6433159) PubChem (31380) PubChem (90820720) PubChem (91240120) PubChem (91519940) PubChem (448437) PubChem (10210008) PubChem (10257404) PubChem (89305995) PubChem (93971688) PubChem (93971689) PubChem (93971690) PubChem (93971691) PubChem (94424892) PubChem (94424893) PubChem (91007743) PubChem (12359017) PubChem (91330154) PubChem (91467158) PubChem (16061195) PubChem (16061196) PubChem (16061204) PubChem (5281243) PubChem (93535598) PubChem (94424894) PubChem (101351905) PubChem (101351908) PubChem (101351909) PubChem (101351910) PubChem (100935514) PubChem (101351907) PubChem (101351906) PubChem (5368396) PubChem (101727094) PubChem (102093134) PubChem (102514741) PubChem (131801656) PubChem (12085680) PubChem (125183271) PubChem (125183272) PubChem (125183273) PubChem (125183613) PubChem (125183614) PubChem (126970006) PubChem (139335388) PubChem (131801655) PubChem (162679657) PubChem (162945700) PubChem (162945708) PubChem (139595700) PubChem (152743345) PubChem (156583347) PubChem (159139983) PubChem (175679236) PubChem (175679086) PubChem (162945701) PubChem (162945702) PubChem (162945703) PubChem (162945704) PubChem (162945705) PubChem (162945706) PubChem (162945707) PubChem (162945709) PubChem (169423521) PubChem (169954357) PubChem (172748694) | |||
| 33 | AP, AX, BAA, BT, BW... (0, g, t, q, d...) | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE | non-polymer | 723.0 | 44 | Chemie (LHG) PubChem (446440) PubChem (46936292) PubChem (73416066) PubChem (65144) PubChem (9547104) PubChem (11846227) PubChem (13305396) PubChem (138986743) | |||
| 34 | AD, AH, BD, BP, BX... (2, A, 0, g, d...) | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE | non-polymer | 787.2 | 86 | Chemie (LMG) | |||
| 35 | IR, LE, UC, WW, YJ... (9, 4, 2, g, G...) | (3R)-beta,beta-caroten-3-ol | non-polymer | 552.9 | 6 | Chemie (RRX) PubChem (20056910) PubChem (92111) PubChem (177443103) PubChem (182237) PubChem (44554791) PubChem (5316150) PubChem (6384256) PubChem (91496173) PubChem (5281235) PubChem (101088204) PubChem (124934401) PubChem (102330248) PubChem (102330249) PubChem (102330250) PubChem (124934402) PubChem (124934403) PubChem (124934404) PubChem (152743353) PubChem (163007083) PubChem (163007084) PubChem (168433814) PubChem (169423484) | |||
| 36 | AK, AT, AZ, BBA, BN... (G, q, r, y, S...) | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL | non-polymer | 600.9 | 22 | Chemie (NEX) PubChem (177697037) PubChem (21158515) PubChem (52948899) PubChem (4481261) PubChem (5282217) PubChem (5320120) PubChem (159749) PubChem (10908146) PubChem (12358959) PubChem (5281247) PubChem (101052392) PubChem (101866355) PubChem (6384259) PubChem (101866356) PubChem (101866357) PubChem (102060371) PubChem (162910894) PubChem (162910891) PubChem (162910895) PubChem (139033583) PubChem (162910892) PubChem (162910893) PubChem (162910896) PubChem (169502056) PubChem (172012198) | |||
| 37 | CT, CX, EK, EM, NR... (q, g, G, R, 9...) | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL | non-polymer | 600.9 | 8 | Chemie (XAT) PubChem (179930) PubChem (24970201) PubChem (448438) PubChem (46936684) PubChem (53477762) PubChem (51346155) PubChem (5282218) PubChem (5315242) PubChem (6384269) PubChem (6442428) PubChem (92096) PubChem (9851662) PubChem (12358665) PubChem (12358669) PubChem (98049828) PubChem (101341888) PubChem (101341890) PubChem (101341892) PubChem (101341893) PubChem (101341894) PubChem (101341895) PubChem (98049827) PubChem (101341889) PubChem (101341891) PubChem (6852159) PubChem (126456015) PubChem (12358664) PubChem (125183415) PubChem (125183416) PubChem (125183417) PubChem (129888894) PubChem (155293357) PubChem (162964874) PubChem (137331554) PubChem (163187351) PubChem (152743429) PubChem (177696491) PubChem (162964869) PubChem (162964870) PubChem (162964871) PubChem (162964872) PubChem (162964873) PubChem (162964875) PubChem (162964876) PubChem (163186889) PubChem (169544055) PubChem (171036315) PubChem (172817291) | |||
| 38 | BK, CP, DZ, EBA, EZ... (G, 0, r, y, s...) | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL | non-polymer | 795.1 | 24 | Chemie (SQD) PubChem (25147486) PubChem (25235342) PubChem (42607399) PubChem (5459390) PubChem (159321) PubChem (9810997) PubChem (9918745) PubChem (481096) PubChem (10219110) PubChem (10373133) PubChem (14463145) PubChem (102201395) PubChem (134765349) | |||
| 39 | ET, JG (a, A) | CA-MN4-O5 CLUSTER | non-polymer | 339.8 | 2 | Chemie (OEX) | |||
| 40 | FT, KG (a, A) | FE (II) ION | non-polymer | 55.8 | 2 | Chemie (FE2) PubChem (27284) | |||
| 41 | GT, HT, LG, MG (a, A) | CHLORIDE ION | non-polymer | 35.5 | 4 | Chemie (CL) PubChem (312) | |||
| 42 | KT, QG, VV, YI (a, A, d, D) | PHEOPHYTIN A | non-polymer | 871.2 | 4 | Chemie (PHO) | |||
| 43 | AAA, CAA, CJ, EX, FBA... (t, v, D, h, z...) | BETA-CAROTENE | non-polymer | 536.9 | 22 | Chemie (BCR) PubChem (573) PubChem (21672398) PubChem (176490061) PubChem (177696266) PubChem (46783370) PubChem (46846294) PubChem (54603957) PubChem (54612003) PubChem (5315709) PubChem (5353436) PubChem (5356616) PubChem (5927371) PubChem (86765360) PubChem (6477957) PubChem (9828626) PubChem (91827292) PubChem (10256668) PubChem (92863346) PubChem (92863347) PubChem (92863348) PubChem (12305639) PubChem (12305640) PubChem (12305642) PubChem (12305644) PubChem (12305647) PubChem (12305652) PubChem (5280489) PubChem (92863345) PubChem (100990628) PubChem (101525094) PubChem (101525095) PubChem (124919640) PubChem (124919639) PubChem (129651951) PubChem (132274419) PubChem (146673260) PubChem (152743364) PubChem (160505766) PubChem (145925599) PubChem (159562859) PubChem (172654026) PubChem (172878405) PubChem (173398668) | |||
| 44 | AW, DJ, QT, YG (d, D, a, A) | 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE | non-polymer | 749.2 | 4 | Chemie (PL9) PubChem (20286) PubChem (23304240) PubChem (21881166) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402) | |||
| 45 | LV, MV, NV, OV, PI... (c, C) | DIGALACTOSYL DIACYL GLYCEROL (DGDG) | non-polymer | 949.3 | 8 | Chemie (DGD) PubChem (24865462) PubChem (24865463) PubChem (448441) PubChem (50904896) PubChem (53480668) PubChem (46936671) PubChem (447899) PubChem (4629344) PubChem (15991538) PubChem (134746152) PubChem (154573294) PubChem (140529801) PubChem (171123158) | |||
| 46 | WV, ZI (d, D) | BICARBONATE ION | non-polymer | 61.0 | 2 | Chemie (BCT) PubChem (769) | |||
| 47 | GW, KJ (e, E) | PROTOPORPHYRIN IX CONTAINING FE | non-polymer | 616.5 | 2 | Chemie (HEM) | |||
| 48 | JY, NK, OL, SV (r, K, R, c) | DODECYL-ALPHA-D-MALTOSIDE | non-polymer | 510.6 | 4 | Chemie (LMU) PubChem (16220143) PubChem (114880) PubChem (24802120) PubChem (25021193) PubChem (44119948) PubChem (445456) PubChem (46936627) PubChem (53393702) PubChem (56845466) PubChem (3481630) PubChem (58112562) PubChem (58253045) PubChem (60087035) PubChem (59615220) PubChem (68322761) PubChem (68338004) PubChem (68441652) PubChem (70796428) PubChem (70813879) PubChem (70839937) PubChem (2802066) PubChem (75487624) PubChem (89796216) PubChem (9849225) PubChem (91094859) PubChem (91608950) PubChem (10413991) PubChem (90817611) PubChem (95566088) PubChem (95566089) PubChem (95566090) PubChem (96327540) PubChem (97038234) PubChem (97038235) PubChem (97294875) PubChem (98046621) PubChem (98046622) PubChem (98046623) PubChem (100976848) PubChem (101111379) PubChem (101111381) PubChem (95566087) PubChem (102565427) PubChem (102219025) PubChem (117716045) PubChem (117753833) PubChem (118443377) PubChem (123281924) PubChem (124184997) PubChem (124196217) PubChem (124196220) PubChem (126735853) PubChem (126735860) PubChem (129720403) PubChem (140505128) PubChem (153835411) PubChem (134694723) PubChem (155885597) PubChem (140479759) PubChem (140841257) PubChem (169619620) PubChem (154810097) PubChem (159812235) PubChem (173767704) PubChem (173885518) PubChem (163184859) | |||
| 49 | ACA, ADA, BCA, CCA, DCA... (R, f1, S, T, Y...) | water | water | 18.0 | 224 | Chemie (HOH) |
Sequence modifications
1, 7: 39 - 252 (UniProt: A0A2P6TPU9)
2, 4, G, 9, q, g: 40 - 261 (UniProt: A0A2P6TDA6)
M, m: -24 - 0 (PDB: 8BD3)
M, m: 1 - 32 (UniProt: A0A5P4NAV9)
| PDB | External Database | Details |
|---|---|---|
| Leu 195 | Phe 719 | conflict |
| Glu 225 | Asp 749 | conflict |
| Asn 250 | Thr 774 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Thr 74 | Ser 64 | conflict |
M, m: 1 - 32 (UniProt: A0A5P4NAV9)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 66 |
| Total formula weight | 1180984.5 | |
| Non-Polymers* | Number of molecules | 672 |
| Total formula weight | 542583.2 | |
| All* | Total formula weight | 1723567.7 |
